[2024-01-25 19:30:36,776] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:30:36,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:30:36,781] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference
[2024-01-25 19:30:37,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:30:37,899] [INFO] Task started: Prodigal
[2024-01-25 19:30:37,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0692bbb-9c62-4728-8fad-55b9ffb2dc4d/GCF_002224365.1_ASM222436v1_genomic.fna.gz | prodigal -d GCF_002224365.1_ASM222436v1_genomic.fna/cds.fna -a GCF_002224365.1_ASM222436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:30:45,787] [INFO] Task succeeded: Prodigal
[2024-01-25 19:30:45,787] [INFO] Task started: HMMsearch
[2024-01-25 19:30:45,787] [INFO] Running command: hmmsearch --tblout GCF_002224365.1_ASM222436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/reference_markers.hmm GCF_002224365.1_ASM222436v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:30:46,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:30:46,001] [INFO] Found 6/6 markers.
[2024-01-25 19:30:46,035] [INFO] Query marker FASTA was written to GCF_002224365.1_ASM222436v1_genomic.fna/markers.fasta
[2024-01-25 19:30:46,036] [INFO] Task started: Blastn
[2024-01-25 19:30:46,036] [INFO] Running command: blastn -query GCF_002224365.1_ASM222436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/reference_markers.fasta -out GCF_002224365.1_ASM222436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:46,568] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:46,570] [INFO] Selected 22 target genomes.
[2024-01-25 19:30:46,570] [INFO] Target genome list was writen to GCF_002224365.1_ASM222436v1_genomic.fna/target_genomes.txt
[2024-01-25 19:30:46,603] [INFO] Task started: fastANI
[2024-01-25 19:30:46,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0692bbb-9c62-4728-8fad-55b9ffb2dc4d/GCF_002224365.1_ASM222436v1_genomic.fna.gz --refList GCF_002224365.1_ASM222436v1_genomic.fna/target_genomes.txt --output GCF_002224365.1_ASM222436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:31:01,994] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:01,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:31:01,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:31:02,006] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:31:02,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:31:02,006] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	100.0	1443	1445	95	conclusive
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	79.6726	599	1445	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.909	173	1445	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.8285	278	1445	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.5015	201	1445	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.3416	225	1445	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.1427	143	1445	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	77.1077	160	1445	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.0397	123	1445	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.962	123	1445	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	76.9258	99	1445	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	76.8111	106	1445	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	76.8103	71	1445	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.6535	89	1445	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.6337	79	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:31:02,009] [INFO] DFAST Taxonomy check result was written to GCF_002224365.1_ASM222436v1_genomic.fna/tc_result.tsv
[2024-01-25 19:31:02,010] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:31:02,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:31:02,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/checkm_data
[2024-01-25 19:31:02,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:31:02,054] [INFO] Task started: CheckM
[2024-01-25 19:31:02,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002224365.1_ASM222436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002224365.1_ASM222436v1_genomic.fna/checkm_input GCF_002224365.1_ASM222436v1_genomic.fna/checkm_result
[2024-01-25 19:31:28,933] [INFO] Task succeeded: CheckM
[2024-01-25 19:31:28,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:31:28,957] [INFO] ===== Completeness check finished =====
[2024-01-25 19:31:28,957] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:31:28,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002224365.1_ASM222436v1_genomic.fna/markers.fasta)
[2024-01-25 19:31:28,958] [INFO] Task started: Blastn
[2024-01-25 19:31:28,958] [INFO] Running command: blastn -query GCF_002224365.1_ASM222436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3ef133f-52de-412b-ae7e-78d32cf208f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002224365.1_ASM222436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:29,646] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:29,649] [INFO] Selected 25 target genomes.
[2024-01-25 19:31:29,649] [INFO] Target genome list was writen to GCF_002224365.1_ASM222436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:31:29,689] [INFO] Task started: fastANI
[2024-01-25 19:31:29,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0692bbb-9c62-4728-8fad-55b9ffb2dc4d/GCF_002224365.1_ASM222436v1_genomic.fna.gz --refList GCF_002224365.1_ASM222436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002224365.1_ASM222436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:31:46,925] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:46,937] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:31:46,937] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002224365.1	s__Virgibacillus_F necropolis	100.0	1443	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002216775.1	s__Virgibacillus_F phasianinus	79.6125	597	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725285.1	s__Virgibacillus sp000725285	78.4521	137	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352005.1	s__Oceanobacillus zhaokaii	77.9963	143	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_902806455.1	s__Lentibacillus doumboii	77.9348	173	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187325.1	s__Virgibacillus_E ndiopensis	77.8535	276	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638995.1	s__Virgibacillus_E oceani	77.5608	228	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908515.1	s__Virgibacillus_I halotolerans	77.485	198	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.3772	148	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	77.35	222	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.3432	184	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008304605.1	s__Oceanobacillus polygoni	77.1771	142	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010993955.1	s__YIM-98839 sp010993955	77.1248	159	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369565.1	s__Oceanobacillus chungangensis	77.0671	120	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	76.962	123	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730295.1	s__LJ137 sp003730295	76.9282	98	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642405.1	s__Pontibacillus salipaludis	76.8653	50	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129865.1	s__Virgibacillus chiguensis	76.8579	107	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.02	97.78	0.91	0.87	3	-
GCF_900114645.1	s__Gracilibacillus orientalis	76.7693	69	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:31:46,940] [INFO] GTDB search result was written to GCF_002224365.1_ASM222436v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:31:46,940] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:31:46,943] [INFO] DFAST_QC result json was written to GCF_002224365.1_ASM222436v1_genomic.fna/dqc_result.json
[2024-01-25 19:31:46,943] [INFO] DFAST_QC completed!
[2024-01-25 19:31:46,943] [INFO] Total running time: 0h1m10s